"It is absolutely the case that we created extreme bad will with Indonesia when we closed down the industry," Barnaby Joyce said.

Deputy Prime Minister Barnaby Joyce has defended his comments linking Australia's suspension of live cattle exports under the Labor Government in 2011 to the subsequent influx of asylum seeker boats.

Appearing on Sunrise on Thursday morning, Joyce said he didn't view the two issues as linked, but the suspension of live cattle exports made negotiations with Indonesia more difficult when more asylum seeker boats arrived.

"I'm just stating the bleeding obvious. You don't want to basically... insult another country by overnight ceasing the supply of a major requirement of their dietary intake which is meat," Joyce said on Wednesday morning.

On Tuesday night, appearing alongside Shadow Agriculture Minister Joel Fitzgibbon and Green's Leader Richard Di Natale at the regional leaders debate in Goulburn, Joyce said that the cessation of the live cattle industry was "around the same time that we started seeing a lot of people arriving in boats".

"You are suggesting that the Indonesian governments unleashed the boats in response... Do you genuinely believe that those two things were linked?" he asked.

And Joyce did not back down.

"I think that our capacity to have a strong relationship with Indonesia is affected by them relying on us as reliable suppliers. It is absolutely the case that we created extreme bad will with Indonesia when we closed down the industry."

Di Natale was quick to seize Joyce's remarks: "What does this have to do with refugees, Barnaby? I'm not seeing the link."

While Joyce wouldn't directly say one caused the other, he reiterated that "the Greens and Labor Party created immense bad will".

Di Natale was quick to shoot back: "Why then did the Indonesians last year dramatically cut back the number of cattle we were receiving? What did you say to them to cause that? You must have said something very nasty."

"We went into close negotiations and they expanded it again. That's how you fix problems," Joyce replied.

— GreensMPs (@GreensMPs) May 25, 2016No doubt, questions are set to follow the Deputy Prime Minister in the coming days.

Labor's Fitzgibbon said a ban would not happen again under a future Labor government, instead referring to regulatory improvements.

But the Greens leader recommitted to his party's policy of ending all live animal exports, arguing the welfare of animals could not be guaranteed once they left our shores. "It's cruel, it's got to stop," he said.

Labor leader Bill Shorten has labelled Joyce's comments "ignorant" and said foreign policy should be left " to the grown ups".

Independent candidate Tony Windsor, who is running against Joyce to reclaim the New England electorate called the Deputy Prime Minister and "unfit leader" who "insulted our nearest neighbour".

"Now what Mr Joyce did last night was prove that he is unfit to be in a leaders' debate."